Saturday, May 8, 2010

Evolutionary Theory: Just Add Water

As many critics have pointed out, evolutionary theory has biased the life sciences with its view of spontaneity. In this universe, things just happen to happen. And that includes the most complicated, least understood thing of all—life. This is the religiously-motivated “just add water” view of biology that makes little scientific sense. Now an evolutionist has appropriately used this very phrase to describe yet another evolutionary take on how life got its start.

New publications from The Center for Chemical Evolution elucidate how peptides can form bilayer membranes with some interesting properties. Could these structures be enlisted to service Darwin's theory? Evolutionists believe life arose spontaneously and so they search for ideas of how this could have occurred. They require several scientifically unlikely events to occur, one of which is the formation of a microscopic compartment in which to hold and safeguard the unlikely chemical combinations that are needed.

Could not the peptide bilayer membranes have provided the compartment? Furthermore, there is the hint that such a membrane, constructed from protein building blocks, could actually perform some protein functions. Perhaps we’re seeing a new pathway to solve thorny problems of how life originated.

Actually what we are seeing is the same old misappropriation of good research—this time with potential nano machinery applications—to junk science. It is yet another in a long list of absurd speculations of how life arose. Did it come from a warm little pond, from the bottom of the sea, or from outer space? Was it DNA or proteins that started things off. No early evolution must have occurred in an RNA world, except that this new research suggests that peptides were the panacea. As one evolutionist explained:

Our studies have now shown that, if you just add water, simple peptides access both the physical properties and the long-range molecular order that is critical to the origins of chemical evolution.

Did you know the most complex thing of all is a piece of cake? Just add water and everything else spontaneously occurs. Religion drives science and it matters.

19 comments:

Scientifically unlikely? Is this a personal belief, or a conclusion of some actual scientific research or calculation you've done? Lipids and peptides spontaneously order.

And since id/creation science deems it unlikely, and already has an answer to origin of life matters, why continue to do any work? What would id/creationist origin of life research be? I guess you all have done the 'peanut butter jar' experiment-give it a year, nothing spontaneously generated, end of story, moving on.

Would "The Center for Chemical Evolution" have been founded, with its important research on nanomaterials, molecular aggregation disorders, and the origin of life? Or do you naively think science can dispose of the evolution and common descent part, and do the research without it?

What are the ID/creation alternatives?How would you state the research into, say Alzheimers fibril formation (which is another focus of this research) as an ID-driven hypothesis? And we're quite often told we can't infer the will of the designer, and you can't detect non-design. How do you state a design hypothesis, when you can't even tell if something is designed or not!!! If it is designed, should we mess with it?

In contrast, evolution reflects that Alzheimer's wouldn't have been selected against in our history, since it is so far post-reproductive. It may be tied to rapid brain evolution:http://harvardscience.harvard.edu/medicine-health/articles/did-rapid-brain-evolution-make-humans-susceptible-alzheimersAnd shared biochemistry (required by evolution, but not guaranteed by design) allows testing in organisms like sea-squirts:http://www.sciencedaily.com/releases/2010/03/100302083451.htm

Another example of the imposition of your religious belief, and how substituting that for actual science is a showstopper.

'Did it come from a warm little pond, from the bottom of the sea, or from outer space?' maybe it was all of these and more.

'Did you know the most complex thing of all is a piece of cake? Just add water and everything else spontaneously occurs' - and this is any more specious than 'magic friend in sky claps hands and life begins' how?

oh, and unless you are a cook with magical powers, you do just add water to cake mix and everything else spontaneously occurs. So what's your point.And again with the 'religion drives science' bit. When are you going to prove this?

This is a surprise to me. I would have thought that a whole cake is more complex than a piece of cake. After all, a whole cake may contain several layers separated by icing, as well as nuts, sprinkles, and other ingredients. A piece, on the other hand, might be just a lump of pure cake. So, I question the reasoning here, and wonder what metric Dr Hunter used to measure complexity.

Cornelius wrote,"Actually what we're seeing is the same old misapproriation of good research.."that's funny, this research was done by the Center for Chemical Evolution, whose goal, as summarized in the same article you linked to is "..integrated research, education and public outreach focused on the chemistry that may have led to the origin of life." so the research was misappropriated by the same evolutionists who actually did the research at an evolutionist center to address evolutionary questions?

As far as I am concerned, the most critical question regarding the origin of life is the origin of the information processing system in the cell.

The cell contains an encoding and decoding scheme that is independent of any laws of physics and chemistry.

Such a system implies that there was a top down approach to the origin of life. An encoding scheme and decoding scheme cannot be developed independently of each other. It is a system engineering problem.

If nature is discovered to be capable of the abstract thought processes that are required to develop the cell's information processing system, that would be an interesting discovery indeed.

"The cell contains an encoding and decoding scheme that is independent of any laws of physics and chemistry."

Really?

Transcription and translation are entirely based on physical and chemical processes. DNA Bases are paired to RNA bases, then codons to anticodons. Hydrogen bonds and shape complementarity.

What independent force do you see acting to make these processes occur?

Note that we can make either happen, in a test tube with purified ingredients. No spark of life or vital force required.

"An encoding scheme and decoding scheme cannot be developed independently of each other."

The cell is not encrypted. The "code" metaphor is just that-popular in the post-WWII cracked-enigma code mind. The idea, with some experimental verification, of self-replicators, and ribozymes would argue this is false. A "coder/decoder" could have even been a single molecule.

As for information processing-lets take something very simple. Salt can exist in two states (really more, but keeping it simple)-dissolved and crystalline. 0 and 1, if you will. When the tide comes in, the well-ordered crystal dissolves. When it goes out, the crystal re-orders.

Now, is the salt 'processing' tidal information in a way that requires creative intelligence? Or is it responding in a physio-chemical manner?

What, then, distinguishes it from a cell, that processes signals in a physio-chemical manner?

RobertC:Transcription and translation are entirely based on physical and chemical processes.

I agree that the processes of transcription and translation require a physical medium in which to operate just as the encoding and decoding processes in a computer require intricately designed logic chips. You are confusing the message with the medium.

A code is an abstract concept that is arbitrary with respect to any laws of physics and chemistry. I am not using the word code in the sense of encryption; I am using it the sense of a sequence of symbols that conveys meaning or specifies a function that is "understood" by both the sender and the receiver. A code is also arbitrary with respect to how it is implemented. The ASCII code for the letter "A" need not be 01000001, for example.

What independent force do you see acting to make these processes occur?

I am merely posing a question that has to be answered for any origin of life scenario to be complete.

"A code is an abstract concept that is arbitrary with respect to any laws of physics and chemistry."

Then the genetic 'code' is not 'code' at all. The physical properties, not any arbitrary meaning, determine how DNA, RNA, and proteins function.

The 'code' is merely chemical. It is neither arbitrary nor independent. It is the correspondence of nucleic acid and amino acids, which, in the process of translation, are coupled by codon/anti-codon pairing. Nothing magic-just base pairing and physical fit.

This is no more a 'code' reflecting intelligence than any receptor binding a ligand or enzyme binding substrate.

Or salt 'decoding' the tides, in my example above. What is the response to that? A binary code-0 or 1 depending on solvent. Strictly physics and chemistry. Does the salt 'understand' the tides independent of physics and chemistry? Is the code abstractly recorded somewhere?

By the way, where is the 'abstract concept'-of the genetic code, that is arbitrary to physics and chemistry recorded? Why is this dispensable in test-tube situations, where we can recapitulate these processes from isolated components? I can't naively know a language, nor can my computer naively execute a program in a language it doesn't know, but a ribosome can naively translate any message provided to it. Where did it learn the arbitrary concept?

RorbertC:Then the genetic 'code' is not 'code' at all. The physical properties, not any arbitrary meaning, determine how DNA, RNA, and proteins function.

I agree that it is the physical properties of the proteins that determine how they function. Proteins consist of a sequence of amino acids that begin as a linear string, and it is only certain sequences that will fold into a functional protein.

What ultimately determines the sequence of amino acids? It is the specific sequence of the nucleotides in the DNA. Note that it is the sequence and not the physical properties of the nucleotides that determine the protein that is to be built.

In other words, what laws of physics and chemistry dictated the particular sequence of nucleotides that is found in DNA as opposed to any other sequence (and why all the redundancy?), and simultaneously created the translation mechanism that converts that sequence into a viable protein?

This is not to say that the physical properties are not important. The elements of the whole encoding/decoding system must be physically compatible for it to work properly.

A sequence of physical elements (or electronic signals) that specifies a certain result (or message) is not like a code; it is a code.

The 'code' is merely chemical. It is neither arbitrary nor independent.

By arbitrary, I mean that there is no reason by virtue of physical or chemical laws that particular nucleotide sequences should specify any particular protein. That is, the particular sequence is independent of any physical laws. Obviously, once a coding system is implemented in a particular physical environment, all the elements in that coding system must be physically compatible.

Or salt 'decoding' the tides, in my example above. What is the response to that? A binary code-0 or 1 depending on solvent. Strictly physics and chemistry. Does the salt 'understand' the tides independent of physics and chemistry? Is the code abstractly recorded somewhere?

No encoding/decoding system "understands" anything. It merely operates by the rules established for it. And I see no encoding/decoding system that depends on a sequence of elements in your salt/tide cycle. As you say, strictly physics and chemistry.

The physical properties of the nucleotide determine the amino acid sequence in translation.

http://en.wikipedia.org/wiki/Translation_%28genetics%29

A tRNA, charged with an amino acids, binds and recognizes RNA nucleotides. This pairing is physico-chemical, and is determines the sequence.

http://en.wikipedia.org/wiki/Transfer_RNA

"I mean that there is no reason by virtue of physical or chemical laws that particular nucleotide sequences should specify any particular protein. That is, the particular sequence is independent of any physical laws."

Doublee writes: "I mean that there is no reason by virtue of physical or chemical laws that particular nucleotide sequences should specify any particular protein. That is, the particular sequence is independent of any physical laws."

Apparently Doublee has absorbed the falsehoods in Stephen Meyer's book "Signature in the Cell," in which he makes a big deal about these alleged facts:

1. A "code" (e.g. genetic code) is arbitrary in the sense that it is determined independent of physical laws;

2. Because a code is arbitrary, only an intelligence can create a code.

Doublee and Stephen Meyer are wrong on both counts. First of all, the genetic code is not arbitary and is largely fixed by physical laws, as shown by recent research into the "stereochemical era" (see below.) The "stereochemical era" is the transition between the RNA-world and the RNA-based protein transcription machinery.

The genetic code is fixed by two physicochemical features. First, RNA molecules bind amino acids; and second, when RANDOM(!) RNA sequences bind amino acids, the RANDOM(!) sequences are far more likely to contain one codon for that amino acid type. For 75% of all types of amino acids, there is at least one codon with a high propensity to be found in RANDOM(!) sequence RNA molecules.

Also: the other codons that code for that amino acid type are constrained (and have been known to be constrained for decades) by the fact that most single-nucleotide mutations will conserve the physicochemical properties (e.g. hydrophobicity or charge) of the encoded amino acid.

Stephen Meyer, in "Signature of the Cell," left this out. IDiot!

Not only that, but even if this weren't true, even if the code were not constrained by chemistry, even if it were arbitrary (it's not), why should we believe that only an intelligence can create an arbitrary code? Total vulgar superstition.

Lastly, why does Dr. Cornelius consider these models "unlikely"? How does he judge "unlikeliness"? Like everybody in the Discovery Institute, he puts on his feathered headdress and uses mystical intuition.

Stephen Meyer's book's predictions (genetic code is arbitrary, no spontaneous formation of nucleotides is possible) have already been falsified. So much for the DI's mystical intuitions about what's "unlikely."

Diogenes says: Also: the other codons that code for that amino acid type are constrained (and have been known to be constrained for decades) by the fact that most single-nucleotide mutations will conserve the physicochemical properties (e.g. hydrophobicity or charge) of the encoded amino acid.

This point can hardly be emphasised enough. The 'arbitrary' genetic code has in fact been shaped by natural selection to minimise the deleterious effects of point mutation, such that the resulting codon typically produces a chemically similar (or the same) amino acid.

Freeland & Hurst (1998) examine this point in some detail, and show that the universal code is robust to natural levels of variance in transition/transversion bias. Their Journal of Molecular Evolution paper is freely available here for those who don't have access to journal databases:http://leitl.org/docs/alife/Doc8.pdf

Interestingly, Cornelius has attempted elsewhere to use this paper as evidence against evolution, contra the authors own conclusions.

Diogenes, just this week I have been given a rather similar line of reasoning (in an older, ongoing thread here):

"It is clear that you have no understanding of how probability works, irregardless of selection. There are nearly an infinity of possible permutations of chemical that go into making life. That fact that there is selection is irrelavant. What you fail to understand is that all the random mutations have to occur before seleection. Unless you are saying there is some mechanism which weeds out the unhelpful combinations before selection. That sounds like ID to me, or perhaps theocratic evolution."

Apparently invoking natural selection as the mechanism for 'weeding out' unhelpful mutatations and combinations of mutations is no longer sufficient - some form of pre-selection selection is inexplicably needed now, which apparently sounds like ID. QED.